chr1-184826645-C-T

Variant names:

• chr1-184826645-C-T
• rs520605
• NM_052966.4:c.718-2903G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_052966.4(NIBAN1):​c.718-2903G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.782 in 152,130 control chromosomes in the GnomAD database, including 47,240 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.78 (47240 hom., cov: 32)
• Consequence: NIBAN1 NM_052966.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.539
• Publications: 4 publications found

Genes affected

NIBAN1 (HGNC:16784): (niban apoptosis regulator 1) This gene encodes a member of the family with sequence similarity 129 protein family. This gene is highly expressed in several cancer cells and may serve as a prognostic marker for certain cancers. The encoded protein may play a role in regulating p53-mediated apoptosis. [provided by RefSeq, Sep 2016]

ENSG00000306770 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.904 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_052966.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NIBAN1	NM_052966.4	MANE Select	c.718-2903G>A		intron	N/A	NP_443198.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NIBAN1	ENST00000367511.4	TSL:1 MANE Select	c.718-2903G>A		intron	N/A	ENSP00000356481.3
	NIBAN1	ENST00000461167.1	TSL:3	n.812-2903G>A		intron	N/A
	NIBAN1	ENST00000487074.5	TSL:5	n.295-3316G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.782 AC: 118893 AN: 152012 Hom.: 47178 Cov.: 32

Gnomad AFR AF: 0.911

Gnomad AMI AF: 0.676

Gnomad AMR AF: 0.749

Gnomad ASJ AF: 0.842

Gnomad EAS AF: 0.619

Gnomad SAS AF: 0.630

Gnomad FIN AF: 0.668

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.751

Gnomad OTH AF: 0.766

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.782 AC: 119011 AN: 152130 Hom.: 47240 Cov.: 32 AF XY: 0.776 AC XY: 57704 AN XY: 74356

African (AFR) AF: 0.911 AC: 37858 AN: 41536

American (AMR) AF: 0.748 AC: 11448 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.842 AC: 2923 AN: 3472

East Asian (EAS) AF: 0.619 AC: 3202 AN: 5172

South Asian (SAS) AF: 0.630 AC: 3037 AN: 4818

European-Finnish (FIN) AF: 0.668 AC: 7040 AN: 10532

Middle Eastern (MID) AF: 0.799 AC: 235 AN: 294

European-Non Finnish (NFE) AF: 0.751 AC: 51033 AN: 67988

Other (OTH) AF: 0.768 AC: 1620 AN: 2110

Alfa AF: 0.759 Hom.: 168826

Bravo AF: 0.792

Asia WGS AF: 0.651 AC: 2264 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.3
DANN	Benign	0.65
PhyloP100		0.54
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs520605; hg19: chr1-184795779;